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Gene functional descriptions offer a crucial line of evidence for candidate genes underlying trait variation. Conversely, plant responses to environmental cues represent important resources to decipher gene function and subsequently provide molecular targets for plant improvement through gene editing. However, biological roles of large proportions of genes across the plant phylogeny are poorly annotated. Here we describe the Joint Genome Institute (JGI) Plant Gene Atlas, an updateable data resource consisting of transcript abundance assays spanning 18 diverse species. To integrate across these diverse genotypes, we analyzed expression profiles, built gene clusters that exhibited tissue/condition specific expression, and tested for transcriptionalmore » response to environmental queues. We discovered extensive phylogenetically constrained and condition-specific expression profiles for genes without any previously documented functional annotation. Such conserved expression patterns and tightly co-expressed gene clusters let us assign expression derived additional biological information to 64 495 genes with otherwise unknown functions. The ever-expanding Gene Atlas resource is available at JGI Plant Gene Atlas (https://plantgeneatlas.jgi.doe.gov) and Phytozome (https://phytozome.jgi.doe.gov/), providing bulk access to data and user-specified queries of gene sets. Combined, these web interfaces let users access differentially expressed genes, track orthologs across the Gene Atlas plants, graphically represent co-expressed genes, and visualize gene ontology and pathway enrichments.« less

With increased demand on freshwater resources for agriculture, it is imperative that more water-use efficient crops are developed. Leaf stable carbon isotope composition, δ¹³C, is a proxy for transpiration efficiency and a possible tool for breeders, but the underlying mechanisms effecting δ¹³C in C₄ plants are not known. It has been suggested that differences in specific leaf area (SLA), which potentially reflects variation in internal CO₂ diffusion, can impact leaf δ¹³C. Furthermore, although it is known that water movement is important for elemental uptake, it is not clear how manipulation of transpiration for increased water-use efficiency may impact nutrient accumulation.more » Here, we characterize the genetic architecture of leaf δ¹³C and test its relationship to SLA and the ionome in five populations of maize. Five significant QTL for leaf δ¹³C were identified, including novel QTL as well as some that were identified previously in maize kernels. One of the QTL regions contains an Erecta-like gene, the ortholog of which has been shown to regulate transpiration efficiency and leaf δ¹³C in Arabidopsis. QTL for δ¹³C were located in the same general chromosome region, but slightly shifted, when comparing data from two different years. Our data does not support a relationship between δ¹³C and SLA, and of the 19 elements analyzed, only a weak correlation between molybdenum and δ¹³C was detected. Together these data add to the genetic understanding of leaf δ¹³C in maize and suggest that improvements to plant water use may be possible without significantly influencing elemental homeostasis.« less

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In order to gain a molecular understanding of the genetic basis for plant traits, we need to be able to identify the underlying gene and the causal allele for genetic loci. Furthermore, this process usually involves a step where a researcher selects likely candidate genes from a list. The process of picking candidate genes is inherently prone to distortion due to human bias, and this is slowing down our research enterprise.

Mechanistic modeling indicates that stomatal conductance could be reduced to improve water use efficiency (WUE) in C₄ crops. Genetic variation in stomatal density and canopy temperature was evaluated in the model C₄ genus, Setaria. Recombinant inbred lines (RILs) derived from a Setaria italica×Setaria viridis cross were grown with ample or limiting water supply under field conditions in Illinois. An optical profilometer was used to rapidly assess stomatal patterning, and canopy temperature was measured using infrared imaging. Stomatal density and canopy temperature were positively correlated but both were negatively correlated with total above-ground biomass. These trait relationships suggest a likely interactionmore » between stomatal density and the other drivers of water use such as stomatal size and aperture. Multiple quantitative trait loci (QTL) were identified for stomatal density and canopy temperature, including co-located QTL on chromosomes 5 and 9. Here, the direction of the additive effect of these QTL on chromosome 5 and 9 was in accordance with the positive phenotypic relationship between these two traits. This, along with prior experiments, suggests a common genetic architecture between stomatal patterning and WUE in controlled environments with canopy transpiration and productivity in the field, while highlighting the potential of Setaria as a model to understand the physiology and genetics of WUE in C₄ species.« less

Genetic selection for whole-plant water use efficiency (yield per transpiration; WUE_plant) in any crop-breeding programme requires high-throughput phenotyping of component traits of WUE_plant such as intrinsic water use efficiency (WUE_i; CO₂ assimilation rate per stomatal conductance). Measuring WUE_i by gas exchange measurements is laborious and time consuming and may not reflect an integrated WUE_i over the life of the leaf. Alternatively, leaf carbon stable isotope composition (δ¹³C_leaf) has been suggested as a potential time-ntegrated proxy for WUE_i that may provide a tool to screen for WUE_plant. However, a genetic link between δ¹³C_leaf and WUE_plant in a C₄ species has notmore » been well established. Thus, to confirm if there is a genetic relationship in a C₄ plant between δ¹³C_leaf and WUE_plant under well watered and water-limited growth conditions, a high-throughput phenotyping facility was used to measure WUE_plant in a recombinant inbred line (RIL) population created between the C₄ grasses Setaria viridis and S. italica . Three quantitative trait loci (QTL) for δ¹³C_leaf were found and co-localized with transpiration, biomass accumulation, and WUE_plant. Additionally, WUE_plant for each of the δ¹³C_leaf QTL allele classes was negatively correlated with δ¹³C_leaf, as would be predicted when WUE_i influences WUE_plant. These findings demonstrate that δ¹³C_leaf is genetically linked to WUE_plant, likely to be through their relationship with WUE_i, and can be used as a high-throughput proxy to screen for WUE_plant in these C₄ species.« less

Plant growth and water use are interrelated processes influenced by genetically controlled morphological and biochemical characteristics. Improving plant water use efficiency (WUE) to sustain growth in different environments is an important breeding objective that can improve crop yields and enhance agricultural sustainability. However, genetic improvement of WUE using traditional methods has proven difficult due to the low throughput and environmental heterogeneity of field settings. To overcome these limitations, this study utilizes a high-throughput phenotyping platform to quantify plant size and water use of an interspecific Setaria italica × Setaria viridis recombinant inbred line population at daily intervals in both well-wateredmore » and water-limited conditions. Our findings indicate that measurements of plant size and water use are correlated strongly in this system; therefore, a linear modeling approach was used to partition this relationship into predicted values of plant size given water use and deviations from this relationship at the genotype level. The resulting traits describing plant size, water use, and WUE all were heritable and responsive to soil water availability, allowing for a genetic dissection of the components of plant WUE under different watering treatments. Linkage mapping identified major loci underlying two different pleiotropic components of WUE. Lastly, this study indicates that alleles controlling WUE derived from both wild and domesticated accessions can be utilized to predictably modulate trait values given a specified precipitation regime in the model C₄ genus Setaria.« less

BTS family members negatively regulate the Fe deficiency response; mutants have increased Fe levels and tolerance to Fe deficiency.

Many important crops are members of the Poaceae family, which develop root systems characterized by a high degree of root initiation from the belowground basal nodes of the shoot, termed the crown. Although this postembryonic shoot-borne root system represents the major conduit for water uptake, little is known about the effect of water availability on its development. Here in this study, we demonstrate that in the model C₄ grass Setaria viridis, the crown locally senses water availability and suppresses postemergence crown root growth under a water deficit. This response was observed in field and growth room environments and in allmore » grass species tested. Luminescence-based imaging of root systems grown in soil-like media revealed a shift in root growth from crown-derived to primary root-derived branches, suggesting that primary root-dominated architecture can be induced in S. viridis under certain stress conditions. Crown roots of Zea mays and Setaria italica, domesticated relatives of teosinte and S. viridis, respectively, show reduced sensitivity to water deficit, suggesting that this response might have been influenced by human selection. Lastly, enhanced water status of maize mutants lacking crown roots suggests that under a water deficit, stronger suppression of crown roots actually may benefit crop productivity.« less